› 3nox

X-ray diffraction
2.34Å resolution

Crystal structure of human DPP-IV in complex with Sa-(+)-(6-(aminomethyl)-5-(2,4-dichlorophenyl)-7-methylimidazo[1,2-a]pyrimidin-2-yl)(morpholino)methanone

Released:
DOI: 10.2210/pdb3nox/pdb
PDB entry 3nox coloured by chain, front view.
PDB entry 3nox coloured by chain, side view.
PDB entry 3nox coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Discovery of 6-(aminomethyl)-5-(2,4-dichlorophenyl)-7-methylimidazo[1,2-a]pyrimidine-2-carboxamides as potent, selective dipeptidyl peptidase-4 (DPP4) inhibitors.
Meng W, Brigance RP, Chao HJ, Fura A, Harrity T, Marcinkeviciene J, O'Connor SP, Tamura JK, Xie D, Zhang Y, Klei HE, Kish K, Weigelt CA, Turdi H, Wang A, Zahler R, Kirby MS, Hamann LG
J Med Chem 53 5620-8 (2010)
PMID: 20684603

Function and Biology Details

Reaction catalysed: 
Release of an N-terminal dipeptide, Xaa-Yaa-|-Zaa-, from a polypeptide, preferentially when Yaa is Pro, provided Zaa is neither Pro nor hydroxyproline.
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-151015 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Dipeptidyl peptidase 4 Chains: A, B
Molecule details ›
Chains: A, B
Length: 753 amino acids
Theoretical weight: 87.45 KDa
Source organism: Homo sapiens
Expression system: Komagataella pastoris
UniProt:
  • Canonical: P27487 (Residues: 39-766; Coverage: 95%)
Gene names: ADCP2, CD26, DPP4
Sequence domains:
Structure domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
3 bound ligands:
Ligand NAG 10 x NAG
Ligand 6A5 2 x 6A5
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: P212121
Unit cell:
a: 65.451Å b: 67.072Å c: 420.443Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.198 0.196 0.264
Expression system: Komagataella pastoris

Quick links

Citations

2 review citations

Novel DPP-4 inhibitors against diabetes.
Liu et al. (2014)
1 more

1 mention without citation

Superior Performance of the SQM/COSMO Scoring Functions in Native Pose Recognition of Diverse Protein-Ligand Complexes in Cognate Docking.
Ajani et al. (2017)